Contacts of the helix formed by residues 1065 - 1079 (chain A) in PDB entry 4DDI
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP1065 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061A TYR* 4.0 8.9 - - + -
1062A ALA* 3.3 25.9 + - + +
1063A GLU 3.2 0.2 - - - -
1064A ASP* 1.3 76.8 - - - +
1066A ASN* 1.3 64.0 + - - +
1067A ILE* 3.2 12.6 - - - +
1068A TYR* 3.3 29.8 - - + +
1069A GLN* 3.0 25.4 + - - +
1238A ARG* 2.8 28.2 + - - -
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Residues in contact with ASN1066 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063A GLU 2.9 24.4 + - - +
1064A ASP* 3.4 10.1 + - - +
1065A ASP* 1.3 71.1 - - - +
1067A ILE* 1.3 62.4 + - - +
1068A TYR 3.2 2.5 - - - -
1069A GLN* 2.9 9.9 + - - +
1070A GLN* 2.9 34.0 + - - +
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Residues in contact with ILE1067 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1064A ASP 5.5 0.7 - - - +
1065A ASP* 3.2 25.6 - - - +
1066A ASN* 1.3 81.7 - - - +
1068A TYR* 1.3 60.1 + - + +
1070A GLN* 3.2 10.4 + - + +
1071A LYS* 3.1 29.1 + - - +
1237A ASP 4.9 2.7 - - - +
1238A ARG* 3.5 41.3 - - - +
1239A GLY 3.5 24.2 - - - +
1240A GLU* 4.0 14.4 - - - +
1241A GLY 4.2 2.7 - - - +
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Residues in contact with TYR1068 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1061A TYR* 3.4 43.1 - + + -
1065A ASP* 3.3 36.7 + - + +
1066A ASN 3.2 0.4 - - - -
1067A ILE* 1.3 80.2 - - + +
1069A GLN* 1.3 60.3 + - - +
1070A GLN 3.0 1.6 - - - -
1071A LYS* 2.9 9.4 + - + +
1072A ILE* 2.8 36.3 + - + +
1236A MET* 4.4 25.4 - - + -
1237A ASP* 3.2 29.4 + - - +
1238A ARG* 3.7 22.0 + - - +
1262A ARG* 5.5 0.4 - - + -
1263A PRO* 3.6 29.5 - - + +
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Residues in contact with GLN1069 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1058A TYR* 2.9 56.5 + - + +
1061A TYR* 4.1 10.1 - - - +
1062A ALA 3.1 15.4 + - - +
1063A GLU* 5.0 6.7 + - - -
1065A ASP 3.0 20.2 + - - +
1066A ASN* 2.9 12.9 + - - +
1068A TYR* 1.3 76.9 - - - +
1070A GLN* 1.3 59.4 + - - +
1072A ILE* 3.5 8.0 + - - +
1073A LYS* 2.9 42.8 + - - +
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Residues in contact with GLN1070 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066A ASN* 2.9 14.1 + - - +
1067A ILE* 3.3 13.9 - - + +
1068A TYR 3.0 0.2 - - - -
1069A GLN* 1.3 74.7 - - - +
1071A LYS* 1.3 64.6 + - - +
1072A ILE 3.1 1.1 - - - -
1073A LYS* 3.4 41.2 - - - +
1074A ASP* 3.0 24.6 + - - +
1241A GLY 5.3 2.9 - - - +
1242A GLY* 4.4 17.5 - - - +
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Residues in contact with LYS1071 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067A ILE* 3.1 20.4 + - - +
1068A TYR* 2.9 14.3 + - + +
1070A GLN* 1.3 78.0 - - - +
1072A ILE* 1.3 56.1 + - - +
1074A ASP* 3.3 5.8 + - - -
1075A LEU* 2.9 21.8 + - - +
1236A MET* 4.0 19.7 - - + +
1237A ASP* 4.0 23.3 - - - +
1238A ARG* 3.5 5.1 - - - +
1239A GLY* 2.4 49.5 + - - +
1241A GLY 3.7 3.8 + - - +
1242A GLY* 4.3 5.1 - - - -
1243A THR 3.1 29.6 - - - +
1244A THR* 3.5 24.9 - - + +
1245A ASN* 5.8 0.4 - - - -
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Residues in contact with ILE1072 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1054A LEU* 4.5 6.5 - - + +
1057A LEU* 3.9 49.6 - - + +
1058A TYR* 3.4 30.2 + - + +
1061A TYR* 4.2 21.3 - - + -
1068A TYR* 2.8 27.2 + - + +
1069A GLN* 3.5 6.0 + - - +
1071A LYS* 1.3 75.2 - - + +
1073A LYS* 1.3 65.3 + - - +
1074A ASP 3.1 1.1 - - - -
1075A LEU* 2.9 8.4 + - + +
1076A HIS* 2.9 25.1 + - + +
1236A MET* 4.5 14.8 - - + -
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Residues in contact with LYS1073 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1058A TYR* 3.5 21.4 + - + +
1069A GLN* 2.9 30.1 + - - +
1070A GLN* 3.4 39.2 - - - +
1072A ILE* 1.3 72.6 - - - +
1074A ASP* 1.3 63.0 + - - +
1076A HIS* 3.1 16.0 + - - +
1077A LYS* 3.1 12.2 + - - +
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Residues in contact with ASP1074 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1070A GLN 3.0 13.8 + - - +
1071A LYS 3.4 4.7 - - - +
1073A LYS* 1.3 75.1 - - - +
1075A LEU* 1.3 57.2 + - - +
1077A LYS* 3.0 36.2 + - - +
1078A LYS* 2.9 37.6 + - - +
1242A GLY* 2.9 32.8 - - - +
1243A THR* 4.4 1.0 - - - -
1244A THR* 3.1 9.5 + - - -
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Residues in contact with LEU1075 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1054A LEU* 3.7 21.1 - - + -
1057A LEU* 4.4 9.0 - - + -
1071A LYS 2.9 10.8 + - - +
1072A ILE* 2.9 12.7 + - + +
1074A ASP* 1.3 76.0 - - - +
1076A HIS* 1.3 62.1 + - - +
1077A LYS 2.9 5.9 + - - -
1078A LYS* 3.1 3.5 + - + -
1079A TYR* 3.0 41.4 + - + +
1234A GLU* 4.2 13.2 - - + +
1236A MET* 3.7 17.9 - - + -
1244A THR* 4.0 20.2 - - + +
1260A LEU* 3.5 26.7 - - + -
1269A LEU* 4.0 15.9 - - + -
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Residues in contact with HIS1076 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1053A GLU* 5.5 3.4 - - + -
1054A LEU* 3.4 29.0 - - + +
1055A SER* 3.3 35.2 + - - -
1058A TYR* 3.6 30.1 - + - +
1072A ILE* 2.9 10.6 + - + +
1073A LYS* 3.1 9.4 + - - +
1075A LEU* 1.3 72.5 - - - +
1077A LYS* 1.3 68.3 + - - +
1079A TYR 3.8 13.7 + - - +
1080A SER* 5.3 3.7 + - - -
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Residues in contact with LYS1077 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1073A LYS 3.1 9.1 + - - -
1074A ASP* 3.0 37.5 + - - +
1075A LEU 2.9 0.2 - - - -
1076A HIS* 1.3 80.5 - - - +
1078A LYS* 1.3 71.2 + - + +
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Residues in contact with LYS1078 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1074A ASP* 2.9 29.5 + - - +
1075A LEU* 3.1 3.7 + - - +
1076A HIS 4.4 0.2 - - - -
1077A LYS* 1.3 88.7 - - + +
1079A TYR* 1.3 88.4 + - + +
1080A SER* 4.2 1.6 + - - -
1234A GLU* 4.5 6.7 - - - +
1244A THR* 2.6 41.1 + - - +
1246A PRO* 5.1 5.9 - - - +
1271A LYS* 3.1 34.0 - - - +
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Residues in contact with TYR1079 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1054A LEU* 3.1 27.7 - - + +
1075A LEU* 3.0 19.6 + - + +
1076A HIS* 3.8 7.1 + - - +
1078A LYS* 1.3 97.2 - - + +
1080A SER* 1.3 61.3 + - - +
1081A TYR 3.5 4.5 - - - +
1232A GLN* 2.8 30.0 + - - +
1234A GLU* 3.1 36.4 + - + +
1258A TYR* 3.8 25.9 - + + -
1269A LEU* 3.7 32.3 - - + -
1270A TYR 3.5 9.9 - - - +
1271A LYS* 3.5 35.7 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il